Description

Usage

1

Arguments

rs_data

RegspliceData object, which has already been
filtered with filterZeros and filterLowCounts.

norm_method

Normalization method to use. Options are "TMM",
"RLE", "upperquartile", and "none". See documentation for
calcNormFactors in edgeR package for details. Default is
"TMM".

Details

Normalization factors are used to scale the raw library sizes (total read counts per
sample). We use the TMM (trimmed mean of M-values) normalization method (Robinson and
Oshlack, 2010), as implemented in the edgeR package.

For more details, see the documentation for calcNormFactors in
the edgeR package.

This step should be performed after filtering with filterZeros and
filterLowCounts. The normalization factors are then used by
limma-voom in the next step (runVoom).

The normalization factors are stored in a new column named norm_factors in the
column meta-data (colData slot) of the RegspliceData
object. The colData can be accessed with the accessor function
colData().

Normalization should be skipped when using exon microarray data. (When using the
regsplice wrapper function, normalization can be disabled with the
argument normalize = FALSE).